Update yfs to use outputs

Signed-off-by: Christopher Hakkaart <chris.hakkaart@seqera.io>

Author: christopher-hakkaart

docs/your-first-script.md

@@ -12,7 +12,7 @@ This guide details fundamental skills to run a basic Nextflow pipeline. It inclu
 
 You will need the following to get started:
 
-- Nextflow: See {ref}`install-page` for installation instructions.
+- Nextflow version 25.10 or later. See {ref}`install-page` for installation instructions. If you have an older version, see {ref}`updating-nextflow` to update.
 
 ## Run a pipeline
 
@@ -25,11 +25,9 @@ params.str = "Hello world!"
 
 // split process
 process split {
-    publishDir "results/lower"
-    
     input:
     val x
-    
+
     output:
     path 'chunk_*'
 
@@ -41,7 +39,6 @@ process split {
 
 // convert_to_upper process
 process convert_to_upper {
-    publishDir "results/upper"
     tag "$y"
 
     input:
@@ -58,9 +55,23 @@ process convert_to_upper {
 
 // Workflow block
 workflow {
-    ch_str = channel.of(params.str)       // Create a channel using parameter input
-    ch_chunks = split(ch_str)             // Split string into chunks and create a named channel
-    convert_to_upper(ch_chunks.flatten()) // Convert lowercase letters to uppercase letters
+    main:
+    ch_str = channel.of(params.str)          // Create a channel using parameter input
+    ch_chunks = split(ch_str)                // Split string into chunks and create a named channel
+    ch_upper = convert_to_upper(ch_chunks.flatten()) // Convert lowercase letters to uppercase letters
+
+    publish:
+    lower = ch_chunks.flatten()
+    upper = ch_upper
+}
+
+output {
+    lower {
+        path 'lower'
+    }
+    upper {
+        path 'upper'
+    }
 }
 ```
 
@@ -71,12 +82,17 @@ This script defines two processes:
 
 The `split` output is emitted as a single element. The `flatten` operator splits this combined element so that each file is treated as a sole element.
 
-The outputs from both processes are published in subdirectories (`lower` and `upper`) in the `results` directory.
+The workflow block is organized into two sections:
+
+- `main:`: defines the workflow logic and how processes are connected via channels
+- `publish:`: declares which channels should be published as workflow outputs
+
+The `output` block (outside the workflow) defines where and how each output should be published. In this example, the outputs from both processes are published in subdirectories (`lower` and `upper`) in the default `results` out directory.
 
 To run your pipeline:
 
-1. Create a new file named `main.nf` in your current directory
-2. Copy and save the above pipeline to your new file
+1. Create a new file named `main.nf` in your current directory.
+2. Copy and save the above pipeline to your new file.
 3. Run your pipeline using the following command:
 
     ```{code-block}
@@ -87,7 +103,7 @@ To run your pipeline:
 You will see output similar to the following:
 
 ```console
- N E X T F L O W   ~  version 24.10.3
+ N E X T F L O W   ~  version 25.10.0
 
 Launching `main.nf` [big_wegener] DSL2 - revision: 13a41a8946
 
@@ -98,6 +114,15 @@ executor >  local (3)
 
 Nextflow creates a `work` directory to store files used during a pipeline run. Each execution of a process is run as a separate task. The `split` process is run as one task and the `convert_to_upper` process is run as two tasks. The hexadecimal string, for example, `82/457482`, is the beginning of a unique hash. It is a prefix used to identify the task directory where the script was executed.
 
+When the pipeline completes, you can view the output files in the `results` directory:
+
+```{code-block} bash
+:class: copyable
+ls -R results/
+```
+
+You will see the published output files organized in the `lower` and `upper` subdirectories.
+
 :::{tip}
 Run your pipeline with `-ansi-log false` to see each task printed on a separate line:
 
@@ -109,7 +134,7 @@ nextflow run main.nf -ansi-log false
 You will see output similar to the following:
 
 ```console
-N E X T F L O W  ~  version 24.10.3
+N E X T F L O W  ~  version 25.10.0
 Launching `main.nf` [peaceful_watson] DSL2 - revision: 13a41a8946
 [43/f1f8b5] Submitted process > split (1)
 [a2/5aa4b1] Submitted process > convert_to_upper (chunk_ab)
@@ -126,13 +151,12 @@ Nextflow tracks task executions in a task cache, a key-value store of previously
 
 You can enable resumability using the `-resume` flag when running a pipeline. To modify and resume your pipeline:
 
-1. Open `main.nf`
+1. Open `main.nf`.
 2. Replace the `convert_to_upper` process with the following:
 
     ```{code-block} groovy
     :class: copyable
     process convert_to_upper {
-        publishDir "results/upper"
         tag "$y"
 
         input:
@@ -148,7 +172,7 @@ You can enable resumability using the `-resume` flag when running a pipeline. To
     }
     ```
 
-3. Save your changes
+3. Save your changes.
 4. Run your updated pipeline using the following command:
 
     ```{code-block} bash
@@ -159,7 +183,7 @@ You can enable resumability using the `-resume` flag when running a pipeline. To
 You will see output similar to the following:
 
 ```console
- N E X T F L O W   ~  version 24.10.3
+ N E X T F L O W   ~  version 25.10.0
 
 Launching `main.nf` [furious_curie] DSL2 - revision: 5490f13c43
 
@@ -190,7 +214,7 @@ You can configure the `str` parameter in your pipeline. To modify your `str` par
 You will see output similar to the following:
 
 ```console
- N E X T F L O W   ~  version 24.10.3
+ N E X T F L O W   ~  version 25.10.0
 
 Launching `main.nf` [distracted_kalam] DSL2 - revision: 082867d4d6